Generating natural phenomena in a virtual world has a number of practical applications. Thanks to the rich and complicated details in the real world, the goal of realistically and efficiently reproducing natural phenomena is well known as an open problem for graphics researchers. In this dissertation, three different issues in modeling liquid animations have been addressed. First, a virtual surface method is proposed to account for surface tension effects and their interactions with solid surfaces in physically based fluid simulation. This allows us to generate various surface tension behaviors in small scale liquid. The second issue that is addressed is how to make small scale fluid simulation more efficient. The proposed solution is a general shallow wave equation model, extended from the original shallow wave equations. By simplifying 3D incompressible fluid dynamics into 2D, small scale liquid can be stably and efficiently simulated over arbitrarily curved surfaces using implicit numerical schemes. The third contribution is a novel hybrid framework that combines image based reconstruction techniques with physically based fluid simulation. While image based methods cannot correctly generate fluid animations alone frame by frame, physics is used as a refinement tool to enforce physical soundness by propagating shape information back and forth in space and time. In this way, water animations can be realistically and faithfully generated from images without error accumulation or stability issues.

This work presents an investigation into the parameter estimation of suspension components and the vertical motions of wheeled vehicles from experimental data. The estimation problems considered were for suspension dampers, a single wheel station and a full vehicle. Using conventional methods (gradient-based (GB), Downhill Simplex (DS)) and stochastic methods (Genetic Algorithm (GA) and Differential Evolution (DE)), three major problems were encountered. These were concerned with the ability and consistency of finding the global optimum solution, time consumption in the estimation process, and the difficulties in setting the algorithm's control parameters. To overcome these problems, a new technique named the discrete variable Hybrid Differential Evolution (dvHDE) method is presented. The new dvHDE method employs an integer-encoding technique and treats all parameters involved in the same unified way as discrete variables, and embeds two mechanisms that can be used to deal with convergence difficulties and reduce the time consumed in the optimisation process. The dvHDE algorithm has been validated against the conventional GB, DS and DE techniques and was shown to be more efficient and effective in all but the simplest cases. Its robustness was demonstrated by its application to a number of vehicle related problems of increasing complexity. These include case studies involving parameter estimation using experimental data from tests on automotive dampers, a single wheel station and a full vehicle. The investigation has shown that the proposed dvHDE method, when compared to the other methods, was the best for finding the global optimum solutions in a short time. It is recommended for nonlinear vehicle suspension models and other similar systems.

Orientador: José Roberto Nunhez / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Química / Made available in DSpace on 2018-08-19T14:59:08Z (GMT). No. of bitstreams: 1 Merendino_EdyMaicon_M.pdf: 4244405 bytes, checksum: c56623b83b7e229872966885f5e9eca5 (MD5) Previous issue date: 2011 / Resumo: As embalagens cartonadas assépticas para alimentos são comuns em nosso dia-a-dia. Tais embalagens são compostas por três materiais: papel, polietileno de baixa densidade e alumínio. Seu processo de reciclagem se dá em duas etapas sucessivas: a reciclagem do papel e a posterior reciclagem do composto de polietileno e alumínio. Durante a primeira etapa de reciclagem, um percentual das fibras de papel não é retirado do composto de polietileno e alumínio o que pode comprometer a qualidade de produtos feitos a partir da reciclagem deste composto. Para a extração do papel residual foi desenvolvido de maneira empírica um equipamento centrífugo em escala industrial. Visando o estudo do funcionamento deste equipamento fez-se a simulação deste usando o método dos elementos discretos (DEM). O primeiro passo foi a determinação de parâmetros físicos e de interação através de experimentos práticos e respectivas simulações computacionais para a calibração de um modelo, o qual foi conseguido de maneira satisfatória. Uma vez tendo o modelo calibrado, foram realizadas simulações com diferentes geometrias para o rotor e parte estática deste equipamento buscando levantar hipóteses para o entendimento do funcionamento do equipamento. Os resultados para diferentes especificações foram comparados e discutidos / Abstract: Milk and beverages carton packages are very common in our lives. These packages are made of three different materials: paper, low density polyethylene and aluminium. The recycling process of these packages takes place in two successive stages: the recycling of paper and the subsequent recycling of polyethylene and aluminium composite. During the first stage of recycling a percentage of the paper is not removed from the composite of polyethylene and aluminium which can compromise the quality of products made from recycling of this composite. An industrial-scale centrifuge equipment was developed empirically for extraction of residual paper. In order to study the operation of this equipment, it was made its simulation using the discrete element method (DEM). The first step was set-up of physical and interaction parameters through practical experiments and computer simulations to calibrate a model, which was achieved satisfactorily. Once the model was calibrated, simulations were performed with different geometries for rotor and static body of this equipment seeking hypotheses in order to understand equipment operation. The results for different specifications were compared and discussed / Mestrado / Processos em Tecnologia Química / Mestre em Engenharia Química

This work presents an investigation into the parameter estimation of suspension components and the vertical motions of wheeled vehicles from experimental data. The estimation problems considered were for suspension dampers, a single wheel station and a full vehicle. Using conventional methods (gradient-based (GB), Downhill Simplex (DS)) and stochastic methods (Genetic Algorithm (GA) and Differential Evolution (DE)), three major problems were encountered. These were concerned with the ability and consistency of finding the global optimum solution, time consumption in the estimation process, and the difficulties in setting the algorithm's control parameters. To overcome these problems, a new technique named the discrete variable Hybrid Differential Evolution (dvHDE) method is presented. The new dvHDE method employs an integer-encoding technique and treats all parameters involved in the same unified way as discrete variables, and embeds two mechanisms that can be used to deal with convergence difficulties and reduce the time consumed in the optimisation process. The dvHDE algorithm has been validated against the conventional GB, DS and DE techniques and was shown to be more efficient and effective in all but the simplest cases. Its robustness was demonstrated by its application to a number of vehicle related problems of increasing complexity. These include case studies involving parameter estimation using experimental data from tests on automotive dampers, a single wheel station and a full vehicle. The investigation has shown that the proposed dvHDE method, when compared to the other methods, was the best for finding the global optimum solutions in a short time. It is recommended for nonlinear vehicle suspension models and other similar systems.

Orientador: José Roberto Nunhez / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Química / Made available in DSpace on 2018-08-18T14:31:01Z (GMT). No. of bitstreams: 1 Spogis_Nicolas_D.pdf: 69966083 bytes, checksum: 554cc0001f4c590e07f36262cc8c616b (MD5) Previous issue date: 2007 / Resumo: Atualmente o ciclo de desenvolvimento de produtos requer um baixo tempo de projeto e mínimos custos. Ao mesmo tempo, a qualidade final do produto não deve ser afetada; pelo contrário, as companhias precisam melhorar seus produtos para se manterem no mercado competitivo. Em muitas indústrias, o uso de software de otimização de projetos está se tornando a principal ferramenta para alcançar rapidamente estas metas aparentemente contraditórias. O projeto de processos químicos e equipamentos é uma tarefa que exige um apoio experimental significante e um grande número de protótipos e testes. Visando reduzir o tempo de desenvolvimento, os softwares ANSYS CFX e modeFRONTIER foram acoplados a fim de obter um projeto de um impelidor de alta eficiência para aplicações "flow-controlled" e para mistura de produtos de baixa viscosidade. A análise de desempenho do impelidor foi realizada através do modelo de turbulência SST (Shear- Stress Transport) acoplado com um modelo de correção para curvatura das linhas de correntes. O modelo SST combina as vantagens dos modelos k- ? e k-?, garantindo uma excelente relação entre a tensão turbulenta e energia cinética turbulenta, além de fornecer uma predição precisa e robusta de descolamentos/separações da camada limite. Os modelos "Multiple Frames of Reference" e "Frozen Rotor Frame Change" foram usados para investigar a interação entre as partes móveis (impelidor) e as partes estáticas (parede do vaso e chicanas) no tanque de mistura. Um algoritmo estocástico robusto (MOGA II) foi utilizado como método de otimização. A otimização multi-objetivo possui sete variáveis de entrada, duas restrições não lineares, e duas funçõesobjetivo. Através deste estudo foi possível obter um aumento simultâneo da capacidade de bombeamento do impelidor e da homogeneidade de mistura / Abstract: Nowadays product development cycle requires shorter turnaround times and lowers costs. At the same time, quality should not suffer; on the contrary, companies need to improve their products in order to remain competitive. In many industries, the use of design optimization software is fast becoming the major way to achieve these apparently conflicting goals. The project of chemical processes and equipments is a task that demands a significant experimental support and a great number of prototypes and tests. Aiming at reducing the development time, ANSYS CFX tools have been successfully coupled to modeFRONTIER so as to lead to an optimal design of a high efficiency impeller for flow-controlled, low viscosity applications. The analysis of impeller shape performance was carried out with the SST (Shear-Stress Transport) model coupled with the streamline curvature turbulence model. The SST model combines the advantages from the k-? and k-? models, ensuring proper relation between turbulent stress and turbulent kinetic energy and allowing accurate and robust prediction of the impeller blade flow separation. The Multiple Frames of Reference and the Frozen Rotor Frame Change model were used in order to investigate the rotor/stator interaction inside the mixing vessel. A robust stochastic algorithm was used for the automatic multi-objective constrained shape design process. The multi-objective function has seven design variables, two nonlinear constraints, and two objective functions. Simultaneous increase of the impeller pumping capacity and mixing vessel homogeneity were achieved using this method / Doutorado / Desenvolvimento de Processos Químicos / Doutor em Engenharia Química

Modeling the free surface flows is important in order to estimate the total drag of the sea Vessels. It is also necessary to study the effects of various maritime maneuvers. In this work, different ways of approximating an unstructured free surface grid with a B-spline surface are investigated. The Least squares and Galerkin approaches are studied in this regard. B-spline nite element method (BSPFEM) is studied for the solution of the steady-state kinematic free surface equation. The volume grid has to be moved in order to match the free boundary when the surface-tracking approach is adopted for the solution of free surface problem. Inherent smoothness of the B-spline representation of the free surface aids this process. B-spline representation of the free surface aids in building viscous volume grids hose boundaries closely match the steady state free surface. The B-spline approximation algorithm and BSPFEM solution of free surface equation have been tested with hypothetical algebraic testcases and real cases such as Gbody, Wigley hull and David Taylor Model Basin(DTMB) 5415 hull series.

This study investigated the influence of the attainable region technique to ball milling as applied in reactor technology. Flow rate, ball filling, mill speed, ball size and mill density were varied. When each was varied, the rest of the parameters were kept constant in-order to determine the influence of each parameter on the process of milling. Selection function and breakage function parameters were selected for the mill model. These were kept constant for all four circuit configurations: open milling circuit, normal closed circuit, reverse closed circuit, and combined closed circuit. Flow rate was varied from 10 tph to 150 tph. It was observed that in all circuit configurations the optimum results were obtained from 90 tph upwards. When ball filling was varied, the optimum results were obtained between 30 % and 40 % of ball filling. At this range the mill is neither experiencing under-filling nor over-filling. When the mill speed was varied, at 60 – 80 % of critical speed the product specification was achieved and for grinding balls, sizes of between 60 mm and 90 mm yielded the optimum results. Varying the mill density resulted in insignificant changes. From the results, the combined closed circuit produced more of the product specification. / School of Engineering / M. Tech. (Engineering: Chemical)

Molecular dynamics (MD) simulations were used to investigate the structural basis for the functions of three proteins: Fc(gamma) receptor III (CD16), von Willebrand factor (VWF), and integrin. CD16, a heavily glycosylated protein expressed on human immune cells, plays a crucial role in immune defense by linking antibody-antigen complexes with cellular effector functions. Glycosylation of CD16 decreases its affinity for IgG. MD simulations were run for CD16-IgG Fc complexes with or without an N-glycan on CD16. The two simulated complexes show different conformations. Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA) approach was used to calculate the binding free energy of the CD16-IgG Fc complexes. The calculated binding free energy helped to identify critical residues. VWF, a multimeric multidomain glycoprotein, initiates platelet adhesion at the sites of vascular injury. A specific VWF metalloprotease, A Disintegrin And Metalloprotease with ThromboSpondin motifs member 13 (ADAMTS-13), cleaves the Tyr1605-Met1606 bond in the VWF A2 domain to generate the full spectrum of plasma VWF species. Shear stress or denaturants assist VWF cleavage by ADAMTS-13 due to the unfolding of A2. MD was used to simulate the unfolding processes of A2 under force or high temperature. The beta-strands of A2 were pulled out sequentially by force, during which the cleavage site changed in steps from the fully buried state to the fully exposed state. Thermal unfolding follows a very different pathway. Integrins are adhesion molecules mediating cell-cell, cell-extracellular matrix, and cell-pathogen interactions. Experiments suggest that integrins can undergo a large-scale change from a bent to an extended conformation, associating with a transition from low to high affinity states, i.e., integrin activation. Steered MD was utilized to simulate the bent-to-extended conformational transition in time of aVb3 integrin. The integrin was observed to change smoothly from the bent to the extended conformation. One major energy barrier was overcome, corresponding to the disruption of the interactions at Hybrid/EGF4/bTD interfaces. A partially extended conformation tends to bend back while a fully extended conformation is stabilized by the coordination of Asp457 with Ca2+ at alpha-genu. Unbending with separated legs overcomes more energy barriers.

Orientador: Denis José Schiozer / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Mecânica / Made available in DSpace on 2018-08-20T08:15:37Z (GMT). No. of bitstreams: 1 Paiva_HernaniPetroni_M.pdf: 4091307 bytes, checksum: 9c0f72cc029a22e1f5a96e7587ad9ab5 (MD5) Previous issue date: 2012 / Resumo: A recuperação de petróleo em reservatórios naturalmente fraturados apresenta-se como um risco de projeto, sobretudo em sistemas molháveis ao óleo ou com molhabilidade intermediária, já que a simulação utilizando deslocamento por injeção de água indica significativa redução da recuperação. As fraturas representam descontinuidades do meio poroso e possuem efeito capilar e condutividade hidráulica distintos, o que altera sensivelmente o comportamento do escoamento no reservatório, e também os mecanismos físicos envolvidos no processo de recuperação. A simulação de reservatórios fraturados é geralmente realizada com o modelo de dupla porosidade, que está implementado nos principais simuladores comerciais. Neste modelo os processos físicos envolvidos na recuperação são representados pela função de transferência entre matriz e fratura. No entanto, os simuladores comerciais utilizam diferentes funções de transferências com diferentes modelos para representar o processo de recuperação. Neste trabalho, foi construído um simulador de dupla porosidade no qual foram implementadas as funções de transferência de Kazemi et al. (1976), Sabathier et al. (1998) e Lu et al. (2008) para comparação dos resultados de recuperação utilizando deslocamento por injeção de água em sistemas molháveis ao óleo ou com molhabilidade intermediária. A comparação entre as funções de transferência foi realizada para diferentes combinações de processos físicos, mostrando que há significativo aumento de recuperação em sistemas molháveis ao óleo ou com molhabilidade intermediária, especialmente em reservatórios totalmente descontínuos quando o deslocamento ocorre por embebição concorrente, coerentemente com o resultado experimental de Firoozabadi (2000). As funções de transferência implementadas, associadas ao modelo de dupla porosidade, foram também comparadas a simuladores comerciais e a um modelo de fraturas discretas refinado, obtendo-se, entretanto, resultados distintos, mostrando que os diferentes modelos de função de transferência fornecem diferentes resultados. A injeção de água mostrou-se um método de recuperação efetivo mesmo em reservatórios totalmente descontínuos em sistemas molháveis ao óleo ou com molhabilidade intermediária quando há deslocamento por embebição concorrente com gradientes de pressão nos blocos de matriz suficientemente elevados. Os resultados são sensíveis aos parâmetros de caracterização e variam de acordo com o processo físico utilizado. Portanto, a caracterização de reservatórios naturalmente fraturados deve ser realizada levando-se em consideração os fenômenos físicos e os modelos utilizados para representá-los / Abstract: The naturally fractured reservoir recovery is a project risk specially in oil-wet or intermediate-wet systems because of the simulations results under waterflood displacement. Fractures are porous medium discontinuities with distinct capillarity and hydraulic conductivity properties that change the reservoir flow behaviour as well the physical mechanisms acting in petroleum recovery. Double-porosity models are generally used in fractured reservoir simulation and have been implemented in the major commercial reservoir simulators. The physical processes acting in petroleum recovery are represented in double-porosity models by matrix-fracture transfer functions. Commercial simulators have their own transfer function implementations, and as a result different kinetics and final recoveries are attained. In this work, a double porosity simulator was built with Kazemi et al. (1976), Sabathier et al. (1998) and Lu et al. (2008) transfer function implementations and their recovery results compared using waterflood displacement in oil-wet or intermediate-wet systems. The results of transfer function comparisons show recovery improvements in oil-wet or intermediate-wet systems under different physical processes combination, particularly in fully discontinuous porous medium when concurrent imbibition takes place, coherent with Firoozabadi (2000) experimental results. Furthermore, the implemented transfer functions, related to a double-porosity model, were compared to double-porosity commercial simulators models, as well a discrete fracture model with refined grid, showing differences between them. Waterflood can be an effective recovery method even in fully discontinuous media for oil-wet or intermediate-wet systems where concurrent imbibition takes place with high enough pressure gradients across the matrix blocks. These results are sensitive to reservoir characterization parameters whose sensitiveness depends on the physical process employed. Naturally fractured reservoir characterization must consider the physical phenomena occurring during recovery and the models used to represent them / Mestrado / Reservatórios e Gestão / Mestre em Ciências e Engenharia de Petróleo

Domain swapping is a wide spread phenomenon which involves the association between two or more protein subunits such that intra-molecular interactions between domains in each subunit are replaced by equivalent inter-molecular interactions between the same domains in different subunits. This thesis is devoted to the analysis of the factors that drive proteins to undergo such association modes. The specific system analyzed is the monomer to swapped dimer formation of the B1 domain of the immunoglobulin G binding protein (GB1). The formation of this dimer was shown to be fostered by 4 amino acid substitutions (L5V, F30V, Y33F, A34F) (Byeon et al. 2003). In this work, computational protein design and molecular dynamics simulations, both with detailed atomic models, were used to gain insight into how these 4 mutations may promote the domain swapping reaction.<p>The stability of the wt and quadruple mutant GB1 monomers was assessed using the software DESIGNER, a fully automatic procedure that selects amino acid sequences likely to stabilize a given backbone structure (Wernisch et al. 2000). Results suggest that 3 of the mutations (L5V, F30V, A34F) have a destabilizing effect. The first mutation (L5V) forms destabilizing interactions with surrounding residues, while the second (F30V) is engaged in unfavorable interactions with the protein backbone, consequently causing local strain. Although the A34F substitution itself is found to contribute favorably to the stability of the monomer, this is achieved only at the expense of forcing the wild type W43 into a highly strained conformation concomitant with the formation of unfavorable interactions with both W43 and V54.<p>Finally, we also provide evidence that A34F mutation stabilizes the swapped dimer structure. Although we were unable to perform detailed protein design calculations on the dimer, due to the lower accuracy of the model, inspection of its 3D structure reveals that the 34F side chains pack against one another in the core of the swapped structure, thereby forming extensive non-native interactions that have no counterparts in the individual monomers. Their replacement by the much smaller Ala residue is suggested to be significantly destabilizing by creating a large internal cavity, a phenomenon, well known to be destabilizing in other proteins. Our analysis hence proposes that the A34F mutation plays a dual role, that of destabilizing the GB1 monomer structure while stabilizing the swapped dimer conformation.<p>In addition to the above study, molecular dynamics simulations of the wild type and modeled quadruple mutant GB1 structures were carried out at room and elevated temperatures (450 K) in order to sample the conformational landscape of the protein near its native monomeric state, and to characterize the deformations that occur during early unfolding. This part of the study was aimed at investigating the influence of the amino acid sequence on the conformational properties of the GB1 monomer and the possible link between these properties and the swapping process. Analysis of the room temperature simulations indicates that the mutant GB1 monomer fluctuates more than its wild type counter part. In addition, we find that the C-terminal beta-hairpin is pushed away from the remainder of the structure, in agreement with the fact that this hairpin is the structural element that is exchanged upon domain swapping. The simulations at 450 K reveal that the mutant protein unfolds more readily than the wt, in agreement with its decreased stability. Also, among the regions that unfold early is the alpha-helix C-terminus, where 2 out of the 4 mutations reside. NMR experiments by our collaborators have shown this region to display increased flexibility in the monomeric state of the quadruple mutant.<p>Our atomic scale investigation has thus provided insights into how sequence modifications can foster domain swapping of GB1. Our findings indicate that the role of the amino acid substitutions is to decrease the stability of individual monomers while at the same time increase the stability of the swapped dimer, through the formation of non-native interactions. Both roles cooperate to foster swapping. / Doctorat en sciences, Spécialisation biologie moléculaire / info:eu-repo/semantics/nonPublished